[2024-01-25 19:04:20,366] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:20,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:20,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg61e77112-01a8-410e-b947-13dcf9da2ca3/dqc_reference
[2024-01-25 19:04:21,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:21,589] [INFO] Task started: Prodigal
[2024-01-25 19:04:21,589] [INFO] Running command: gunzip -c /var/lib/cwl/stge21891d5-0496-4b9b-ad35-77b4ad5b44e4/GCF_014855495.1_ASM1485549v1_genomic.fna.gz | prodigal -d GCF_014855495.1_ASM1485549v1_genomic.fna/cds.fna -a GCF_014855495.1_ASM1485549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:38,372] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:38,373] [INFO] Task started: HMMsearch
[2024-01-25 19:04:38,373] [INFO] Running command: hmmsearch --tblout GCF_014855495.1_ASM1485549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61e77112-01a8-410e-b947-13dcf9da2ca3/dqc_reference/reference_markers.hmm GCF_014855495.1_ASM1485549v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:38,641] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:38,643] [INFO] Found 6/6 markers.
[2024-01-25 19:04:38,681] [INFO] Query marker FASTA was written to GCF_014855495.1_ASM1485549v1_genomic.fna/markers.fasta
[2024-01-25 19:04:38,681] [INFO] Task started: Blastn
[2024-01-25 19:04:38,681] [INFO] Running command: blastn -query GCF_014855495.1_ASM1485549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61e77112-01a8-410e-b947-13dcf9da2ca3/dqc_reference/reference_markers.fasta -out GCF_014855495.1_ASM1485549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:39,323] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:39,326] [INFO] Selected 26 target genomes.
[2024-01-25 19:04:39,326] [INFO] Target genome list was writen to GCF_014855495.1_ASM1485549v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:39,374] [INFO] Task started: fastANI
[2024-01-25 19:04:39,374] [INFO] Running command: fastANI --query /var/lib/cwl/stge21891d5-0496-4b9b-ad35-77b4ad5b44e4/GCF_014855495.1_ASM1485549v1_genomic.fna.gz --refList GCF_014855495.1_ASM1485549v1_genomic.fna/target_genomes.txt --output GCF_014855495.1_ASM1485549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:57,969] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:57,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61e77112-01a8-410e-b947-13dcf9da2ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:57,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61e77112-01a8-410e-b947-13dcf9da2ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:57,984] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:57,984] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:57,985] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	100.0	1475	1478	95	conclusive
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	80.0137	545	1478	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	79.3996	203	1478	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	79.1748	196	1478	95	below_threshold
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	78.1571	138	1478	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	77.6155	127	1478	95	below_threshold
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	77.4967	163	1478	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	77.3053	114	1478	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	77.1432	232	1478	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	77.1	252	1478	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	77.0849	265	1478	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	77.057	164	1478	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	77.0421	227	1478	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	77.0336	270	1478	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	77.0102	226	1478	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.8698	107	1478	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.73	151	1478	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.724	144	1478	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.7136	138	1478	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	76.6959	148	1478	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.6775	114	1478	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.6634	143	1478	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.5801	186	1478	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	76.5204	61	1478	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	76.4979	61	1478	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.0836	123	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:57,986] [INFO] DFAST Taxonomy check result was written to GCF_014855495.1_ASM1485549v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:57,986] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:57,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:57,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61e77112-01a8-410e-b947-13dcf9da2ca3/dqc_reference/checkm_data
[2024-01-25 19:04:57,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:58,029] [INFO] Task started: CheckM
[2024-01-25 19:04:58,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014855495.1_ASM1485549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014855495.1_ASM1485549v1_genomic.fna/checkm_input GCF_014855495.1_ASM1485549v1_genomic.fna/checkm_result
[2024-01-25 19:05:44,735] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:44,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:44,755] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:44,756] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:44,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014855495.1_ASM1485549v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:44,756] [INFO] Task started: Blastn
[2024-01-25 19:05:44,756] [INFO] Running command: blastn -query GCF_014855495.1_ASM1485549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61e77112-01a8-410e-b947-13dcf9da2ca3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014855495.1_ASM1485549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:45,663] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:45,666] [INFO] Selected 17 target genomes.
[2024-01-25 19:05:45,666] [INFO] Target genome list was writen to GCF_014855495.1_ASM1485549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:45,678] [INFO] Task started: fastANI
[2024-01-25 19:05:45,679] [INFO] Running command: fastANI --query /var/lib/cwl/stge21891d5-0496-4b9b-ad35-77b4ad5b44e4/GCF_014855495.1_ASM1485549v1_genomic.fna.gz --refList GCF_014855495.1_ASM1485549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014855495.1_ASM1485549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:59,397] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:59,408] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:59,408] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014855495.1	s__Euzebyella saccharophila	100.0	1475	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014349235.1	s__Euzebyella sp014349235	92.3002	1256	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855515.1	s__Euzebyella marina	80.0108	544	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_002269385.1	s__Maribacter cobaltidurans	79.3996	203	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017810075.1	s__Pseudozobellia sp017810075	78.9527	469	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	78.691	127	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813285.1	s__Pseudozobellia sp002813285	78.4729	428	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141855.1	s__Pseudozobellia thermophila	77.6485	297	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	77.6155	127	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_008367235.1	s__Pareuzebyella sediminis	77.5146	162	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pareuzebyella	95.0	99.39	99.39	0.97	0.97	2	-
GCF_900156625.1	s__Zobellia uliginosa	77.1923	221	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330125.1	s__Zobellia sp015330125	77.0314	228	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.724	144	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009184425.1	s__Muricauda olearia	76.6775	114	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_001447995.1	s__Maribacter dokdonensis	76.5801	186	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_000423405.1	s__Mesonia mobilis	76.4979	61	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900102165.1	s__Cellulophaga baltica	76.0836	123	1478	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:59,409] [INFO] GTDB search result was written to GCF_014855495.1_ASM1485549v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:59,411] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:59,414] [INFO] DFAST_QC result json was written to GCF_014855495.1_ASM1485549v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:59,414] [INFO] DFAST_QC completed!
[2024-01-25 19:05:59,414] [INFO] Total running time: 0h1m39s